Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency

Citation: Serba, D. D., Uppalapati, S. R., Krom, N., Mukherjee, S., Tang, Y. H., Mysore, K. S., & Saha, M. C. (2016). Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency. Bmc Genomics, 17, 14. doi:10.1186/s12864-016-3377-8Background: Switchgrass, a warm-season perennial grass studied as a potential dedicated biofuel feedstock, is classified into two main taxa - lowland and upland ecotypes - that differ in morphology and habitat of adaptation. But there is limited information on their inherent molecular variations. Results: Transcriptome analysis by RNA-sequencing (RNA-Seq) was conducted for lowland and upland ecotypes to document their gene expression variations. Mapping of transcriptome to the reference genome (Panicum virgatum v1. 1) revealed that the lowland and upland ecotypes differ substantially in sets of genes transcribed as well as levels of expression. Differential gene expression analysis exhibited that transcripts related to photosynthesis efficiency and development and photosystem reaction center subunits were upregulated in lowlands compared to upland genotype. On the other hand, catalase isozymes, helix-loop-helix, late embryogenesis abundant group I, photosulfokinases, and S-adenosyl methionine synthase gene transcripts were upregulated in the upland compared to the lowlands. At >= 100x coverage and >= 5% minor allele frequency, a total of 25,894 and 16,979 single nucleotide polymorphism (SNP) markers were discovered for VS16 (upland ecotype) and K5 (lowland ecotype) against the reference genome. The allele combination of the SNPs revealed that the transition mutations are more prevalent than the transversion mutations. Conclusions: The gene ontology (GO) analysis of the transcriptome indicated lowland ecotype had significantly higher representation for cellular components associated with photosynthesis machinery controlling carbon fixation. In addition, using the transcriptome data, SNP markers were detected, which were distributed throughout the genome. The differentially expressed genes and SNP markers detected in this study would be useful resources for traits mapping and gene transfer across ecotypes in switchgrass breeding for increased biomass yield for biofuel conversion

Human Umbilical Cord Matrix Mesenchymal Stem Cells Suppress the Growth of Breast Cancer by Expression of Tumor Suppressor Genes

Citation: Ohta, N., Ishiguro, S., Kawabata, A., Uppalapati, D., Pyle, M., Troyer, D., . . . Tamura, M. (2015). Human Umbilical Cord Matrix Mesenchymal Stem Cells Suppress the Growth of Breast Cancer by Expression of Tumor Suppressor Genes. Plos One, 10(5), 17. doi:10.1371/journal.pone.0123756Human and rat umbilical cord matrix mesenchymal stem cells (UCMSC) possess the ability to control the growth of breast carcinoma cells. Comparative analyses of two types of UCMSC suggest that rat UCMSC-dependent growth regulation is significantly stronger than that of human UCMSC. Their different tumoricidal abilities were clarified by analyzing gene expression profiles in the two types of UCMSC. Microarray analysis revealed differential gene expression between untreated naive UCMSC and those co-cultured with species-matched breast carcinoma cells. The analyses screened 17 differentially expressed genes that are commonly detected in both human and rat UCMSC. The comparison between the two sets of gene expression profiles identified two tumor suppressor genes, adipose-differentiation related protein (ADRP) and follistatin (FST), that were specifically up-regulated in rat UCMSC, but down-regulated in human UCMSC when they were co-cultured with the corresponding species' breast carcinoma cells. Over-expression of FST, but not ADRP, in human UCMSC enhanced their ability to suppress the growth of MDA-231 cells. The growth of MDA-231 cells was also significantly lower when they were cultured in medium conditioned with FST, but not ADRP over-expressing human UCMSC. In the breast carcinoma lung metastasis model generated with MDA-231 cells, systemic treatment with FST-over-expressing human UCMSC significantly attenuated the tumor burden. These results suggest that FST may play an important role in exhibiting stronger tumoricidal ability in rat UCMSC than human UCMSC and also implies that human UCMSC can be transformed into stronger tumoricidal cells by enhancing tumor suppressor gene expression

Renormalization group approach to the normal phase of 2D Fermi gases

We present results on the effect of short-range, attractive interactions on the properties of balanced 2D Fermi gases in the non-superfluid (normal) phase. Our approach combines the renormalization group (RG) with perturbation theory, yielding observables such as the equation of state and compressibility. We find good agreement with recent experiments that measured the equation of state in trapped gases in the balanced regime, showing that these results are consistent with logarithmic corrections in the equation of state.Comment: 7 pages, 4 figure

ASSESSMENT OF THE NUTRITIONAL BEHAVIOUR AMONG COLLEGE STUDENTS-A SURVEY

Objective: To assess the nutritional behaviour among college students.Methods: A prospective observational survey was conducted randomly among college students in Guntur. A self-administered data collection form was designed to understand the nutritional behaviour of the subjects.Results: A total of 300 subjects were included in the study, among them 225(75%) were females and 75(25%) were males. The survey revealed that most of them skipped their meals. A majority of 184(61.33%) students opted for high-fat diet and 268(89.33%) opted for starch-rich foods. A total of 222(74%) students usually eat four different varieties of vegetables but only 71(23.66%) of them eat fruits in each week.Conclusion: From this study, it was evident that majority of students have poor dietary habits. Lack of awareness on balanced diet and due to their busy schedules, teenagers were not maintaining a proper diet. This could be reduced by bringing minimum awareness on dietary habits to them. Taking proper diet is very essential to reduce the risk of diseases in future and to improve nourishment

Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass

Abstract Background Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significantly reduce switchgrass biomass yield. Despite its importance as a prominent bioenergy crop, a genome-wide comprehensive analysis of NB-LRR disease resistance genes has yet to be performed in switchgrass. Results In this study, we used a homology-based computational approach to identify 1011 potential NB-LRR resistance gene homologs (RGHs) in the switchgrass genome (v 1.1). In addition, we identified 40 RGHs that potentially contain unique domains including major sperm protein domain, jacalin-like binding domain, calmodulin-like binding, and thioredoxin. RNA-sequencing analysis of leaf tissue from ‘Alamo’, a rust-resistant switchgrass cultivar, and ‘Dacotah’, a rust-susceptible switchgrass cultivar, identified 2634 high quality variants in the RGHs between the two cultivars. RNA-sequencing data from field-grown cultivar ‘Summer’ plants indicated that the expression of some of these RGHs was developmentally regulated. Conclusions Our results provide useful insight into the molecular structure, distribution, and expression patterns of members of the NB-LRR gene family in switchgrass. These results also provide a foundation for future work aimed at elucidating the molecular mechanisms underlying disease resistance in this important bioenergy crop

Expression profiling during arabidopsis/downy mildew interaction reveals a highly-expressed effector that attenuates responses to salicylic acid

Plants have evolved strong innate immunity mechanisms, but successful pathogens evade or suppress plant immunity via effectors delivered into the plant cell. Hyaloperonospora arabidopsidis (Hpa) causes downy mildew on Arabidopsis thaliana, and a genome sequence is available for isolate Emoy2. Here, we exploit the availability of genome sequences for Hpa and Arabidopsis to measure gene-expression changes in both Hpa and Arabidopsis simultaneously during infection. Using a high-throughput cDNA tag sequencing method, we reveal expression patterns of Hpa predicted effectors and Arabidopsis genes in compatible and incompatible interactions, and promoter elements associated with Hpa genes expressed during infection. By resequencing Hpa isolate Waco9, we found it evades Arabidopsis resistance gene RPP1 through deletion of the cognate recognized effector ATR1. Arabidopsis salicylic acid (SA)-responsive genes including PR1 were activated not only at early time points in the incompatible interaction but also at late time points in the compatible interaction. By histochemical analysis, we found that Hpa suppresses SA-inducible PR1 expression, specifically in the haustoriated cells into which host-translocated effectors are delivered, but not in non-haustoriated adjacent cells. Finally, we found a highly-expressed Hpa effector candidate that suppresses responsiveness to SA. As this approach can be easily applied to host-pathogen interactions for which both host and pathogen genome sequences are available, this work opens the door towards transcriptome studies in infection biology that should help unravel pathogen infection strategies and the mechanisms by which host defense responses are overcome

Is there a positive effect of participation on a clinical trial for patients with advanced non-small cell lung cancer?

Background: There is general belief that patients who enrolled on a clinical trial have better outcomes compared to those who are treated outside of a trial. We analyzed if there was a \u2032trial effect\u2032 for patients with advanced non-small cell lung cancer (NSCLC) treated with chemotherapy. Materials and methods: A retrospective analysis of cohorts of patients with advanced NSCLC who received chemotherapy inside and outside of a clinical trial were analyzed for response rates (RR), progression free survival (PFS), overall survival (OS), 1 and 2 year survival. Results: There were 194 patients who received chemotherapy of which, 54 were on a clinical trial and 140 outside of it. For the whole group, the RR, median PFS, OS, one and two-year survivals were 35.4%, six months (range, 2-70), seven months (range, 2-72), 29.8% and 9.7% respectively. The differences in RR and PFS of patients who were treated inside and outside of a clinical trial were not significant (P=0.6164, 0.0881). The differences in median OS and one-year survivals between the groups were significant (P=0.0052, 0.022). For the whole group, patients who received II line chemotherapy had better OS (P\ua30.0001). More patients in the trial group received II line chemotherapy (P=0.0004).The difference in the median OS between the groups continued to be significant even after patients who received II line chemotherapy were censored (P=0.0437). Conclusion: Patients with advanced NSCLC who were treated inside of a clinical trial had better OS compared to those who were treated outside of it